Mercurial > repos > bimib > cobraxy

diff COBRAxy/custom_data_generator.py @ 25:80bfd8743ea6 draft

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Uploaded
author luca_milaz
date Thu, 19 Sep 2024 08:06:59 +0000
parents 20c30b1a032d
children 4c9ade74c4d7
line wrap: on
line diff
--- a/COBRAxy/custom_data_generator.py	Thu Sep 19 08:03:37 2024 +0000
+++ b/COBRAxy/custom_data_generator.py	Thu Sep 19 08:06:59 2024 +0000
@@ -188,15 +188,11 @@
     bounds = generate_bounds(model)
     medium = get_medium(model)
 
-    rulesPath     = utils.FilePath("rules", "csv")
-    reactionsPath = utils.FilePath("reactions", "csv")
-    boundsPath = utils.FilePath("bounds", "csv")
-    mediumPath = utils.FilePath("medium", "csv")
 
-    save_as_csv(rules, rulesPath, ("ReactionID", "Rule"))
-    save_as_csv(reactions, reactionsPath, ("ReactionID", "Reaction"))
-    bounds.to_csv(boundsPath.show(), sep = '\t')
-    medium.to_csv(mediumPath.show(), sep = '\t')
+    save_as_csv(rules, ARGS.out_rules, ("ReactionID", "Rule"))
+    save_as_csv(reactions, ARGS.out_reactions, ("ReactionID", "Reaction"))
+    bounds.to_csv(ARGS.out_bounds, sep = '\t')
+    medium.to_csv(ARGS.out_medium, sep = '\t')
 
 
     # ^ Please if anyone works on this after updating python to 3.12 change the if/elif into a match statement!!